Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_galaxy_tree.py @ 25:573136f142b6 draft

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planemo upload
author jjjjia
date Wed, 29 Aug 2018 15:10:44 -0400
parents e5a7da2239af
children 3dc84625d22c
comparison
equal deleted inserted replaced
24:e5a7da2239af 25:573136f142b6
94 self.MLSTSpecies = "?" 94 self.MLSTSpecies = "?"
95 self.SequenceType = "?" 95 self.SequenceType = "?"
96 self.MLSTScheme = "?" 96 self.MLSTScheme = "?"
97 self.CarbapenemResistanceGenes ="?" 97 self.CarbapenemResistanceGenes ="?"
98 self.plasmidBestMatch ="?" 98 self.plasmidBestMatch ="?"
99 self.plasmididentity =-1 99 self.plasmididentity =-1
100 self.plasmidsharedhashes ="?" 100 self.plasmidsharedhashes ="?"
101 self.OtherAMRGenes="?" 101 self.OtherAMRGenes="?"
102 self.TotalPlasmids = -1 102 self.TotalPlasmids = -1
103 self.plasmids = [] 103 self.plasmids = []
104 self.DefinitelyPlasmidContigs ="?" 104 self.DefinitelyPlasmidContigs ="?"
105 self.LikelyPlasmidContigs="?" 105 self.LikelyPlasmidContigs="?"
182 _results.MLSTScheme = (str(r.loc[r.index[i], 'MLST Scheme'])) 182 _results.MLSTScheme = (str(r.loc[r.index[i], 'MLST Scheme']))
183 _results.CarbapenemResistanceGenes = (str(r.loc[r.index[i], 'Carbapenem Resistance Genes'])) 183 _results.CarbapenemResistanceGenes = (str(r.loc[r.index[i], 'Carbapenem Resistance Genes']))
184 _results.OtherAMRGenes = (str(r.loc[r.index[i], 'Other AMR Genes'])) 184 _results.OtherAMRGenes = (str(r.loc[r.index[i], 'Other AMR Genes']))
185 _results.TotalPlasmids = int(r.loc[r.index[i], 'Total Plasmids']) 185 _results.TotalPlasmids = int(r.loc[r.index[i], 'Total Plasmids'])
186 _results.plasmidBestMatch = str(r.loc[r.index[i], 'Plasmid Best Match']) 186 _results.plasmidBestMatch = str(r.loc[r.index[i], 'Plasmid Best Match'])
187 _results.plasmididentity = str(r.loc[r.index[i], 'Plasmid Identity']) 187 _results.plasmididentity = str(r.loc[r.index[i], 'Plasmid Identity'])
188 _results.plasmidsharedhashes = float(r.loc[r.index[i], 'Plasmid Shared Hash']) 188 _results.plasmidsharedhashes = float(r.loc[r.index[i], 'Plasmid Shared Hash'])
189 for j in range(0,_results.TotalPlasmids): 189 for j in range(0,_results.TotalPlasmids):
190 _plasmid = plasmidObj() 190 _plasmid = plasmidObj()
191 _plasmid.PlasmidsID =(((str(r.loc[r.index[i], 'Plasmids ID'])).split(";"))[j]) 191 _plasmid.PlasmidsID =(((str(r.loc[r.index[i], 'Plasmids ID'])).split(";"))[j])
192 _plasmid.Num_Contigs = (((str(r.loc[r.index[i], 'Num_Contigs'])).split(";"))[j]) 192 _plasmid.Num_Contigs = (((str(r.loc[r.index[i], 'Num_Contigs'])).split(";"))[j])